


The Alternates

by Yosituna



Category: Mass Effect
Genre: AU, Alternate Universe
Language: English
Status: In-Progress
Published: 2013-05-31
Updated: 2013-06-01
Packaged: 2017-12-13 12:23:23
Rating: Teen And Up Audiences
Warnings: Major Character Death
Chapters: 2
Words: 3,594
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/824279
Author URL: https://archiveofourown.org/users/Yosituna/pseuds/Yosituna
Summary: <blockquote class="userstuff">
              <p>The Lazarus Project has failed. The man who was to save the galaxy, Commander Shepard, once again lies dead on the Lazarus Research Station, riddled with bullets by rogue security mechs. It’s now up to a small band of people led by Kaidan Alenko and Liara T’Soni—old friends, new allies, and possibly even a few former enemies—to somehow find a way to defeat the Collectors and wage an increasingly hopeless war against the Reapers.</p>
            </blockquote>





	1. The Death of Hope

**Summary for the Chapter:**

> The attack from within the Lazarus Research Station catches Miranda Lawson and Jacob Taylor unprepared.

_Approximately 0200 hours_  
_March 13, 2185_  
_Lazarus Research Station_

The medical lab was dimly lit and still. On an examination table in the middle of the room, directly underneath several large pieces of machinery suspended from the ceiling, lay a man. A bank of computers on the far side of the large room shed a diffuse light, casting shadows on the small beds nearby and on the man lying on the table. The only other source of light was a faint reddish-orange glow, which seemed to come from several visible scars on his face. The slow movement of his chest as he breathed was the only motion in the room.

The silence was broken by the faint sound of distant gunfire. Several human-sounding screams were cut horribly short. Soon the shots, and the screams, grew closer. Laser sights and the flickering glow of an electrical fire were soon visible through the window, had anyone cared to look.

Suddenly the lights in the lab flared on, and the intercom system above the supine man buzzed to life.

"Wake up, Commander."

The figure lying on the examination table did not move, his chest continuing a steady rise and fall.

"Shepard, do you hear me? Get out of that bed, _now_ —this facility is under attack."

Nothing changed. The gunfire drew closer.

* * *

Miranda made a sound of frustration. _Shit. He’s not ready yet!_ The flickering viewscreen on her terminal showed Shepard, still lying motionless in the med lab. A few swipes of her finger shrank the image and brought up several other security feeds. Most showed static but a few showed either blood-covered human corpses or quietly whirring security mechs, stalking the facility for more "intruders."

One of the areas with mechs was dangerously close to the med lab, only a room or two away. _Dammit! If any of those make it to Shepard, the Project—everything I’ve worked for over the past two years—is ruined!_

Mind racing, she changed her comm channel. "Jacob! Do you read me?" A low static was her only reply. Still, maybe the communication problem was just one-way. "Jacob, if you're hearing this, Shepard is in danger. He’s not responding to warnings, and the security mechs are getting close to his position. Get to the med lab ASAP and do whatever you have to to keep him alive! I’m heading out to try to do the same. If you get to the lab and neither Shepard nor I are there, then meet us at the shuttles." Her voice was measured and almost hid the underlying panic.

With that, Miranda dropped the comm unit in disgust. She reached out and swiped at the screen, expanding a visual of the area outside her door. Only one mech. Good. She checked the thermal clip on her pistol and grabbed several more from her desk. _Hope this is enough to get me through to Shepard and to the docking bay. Hope Shepard stays alive long enough for it to matter._

* * *

The door hissed open, safety locks automatically bypassed by another part of the security system. The LOKI mech moved inside. It noted one intruder, located on the examination table. Human, male, Caucasian, approximately thirty years old. Identity: Lieutenant Commander John Shepard of the Systems Alliance, deceased. The human was unmoving and possibly unconscious, but infrared readings showed that the identity record was in error. He was alive. Therefore, a threat.

The mech opened fire.

* * *

Jacob rounded the corner and the lab came into sight. _Shit! The door is open! Did Shepard escape, or…_

His heart sank as he heard the whirr of servos from within. Without further thought, Jacob dove into the room, rolling as he hit the ground. The mech sprayed the ground where he’d been with bullets, but before it could reorient Jacob hit it with a combo of gunfire and biotics, rendering it very quickly into inert pieces of scrap.

He looked at the examination table, knowing the worst had happened. It was covered in blood and thicker things, but no Shepard. Jacob had a brief moment of hope until he realized that the impact of the bullets had shoved Shepard’s body off the table and onto the floor. And it was nothing but a body...Jacob quickly knelt and checked for Shepard’s pulse just to make sure, but felt nothing. The blood loss was severe; the body had been riddled with bullets, and clearly at least one of those bullets had severed an artery. Shepard’s clothing was blood-soaked shreds, and his body looked like nothing so much raw meat with bits of metal sprinkled throughout.

_Damn. I don’t suppose they can bring him back again…or can they? Shepard is important. Without him, this entire galaxy is screwed._

With a sigh, he rose to his feet. He heard distant gunfire, coming closer. Sounded like a heavy pistol. _Miranda. Should have known she’d survive. And man, but she is NOT going to be happy._

* * *

When the lab door came into sight, Miranda saw Jacob standing in the doorway, gun raised. He lowered it when he recognized her. Her instinctive sense of relief fled when she realized that she didn’t see Shepard anywhere.

"Jacob! Is Shepard...?"

Jacob sighed and shook his head. "I got here as soon as I could, but..."

"Dammit!" Miranda felt like kicking something, but knew it would do no good.

Turning back, she went to the wall-mounted security console next to the door she’d come through and pried it open. Ripping out one wire and plugging another into a separate coupling, she then stood back and worked on her omni-tool for a moment, then closed it out.

"There, that should keep the mechs off our backs. It’s no longer hooked into the main security system, so the mechs shouldn't be able to access it, but I can open it with my omni-tool when we need to leave." Turning back, she walked towards Jacob, who was still standing in the lab doorway. "Now, show me Shepard."

When she caught sight of the bloody mass, her eyes narrowed. " _Shit_. That's two years and four billion credits, down the drain."

"The Lazarus Project brought him back once already—mostly. Could you do it again?"

"Maybe. It'll be difficult without Wilson, and I'm not sure whether the Illusive Man is likely to give us another four billion credits." She chuckled, but no humor reached her eyes. "I'm not sure he has that much to give, especially with what he’s already spent on the SR-2."

Jacob’s brow furrowed as he processed Miranda’s passing comment. “Wait, Wilson? Did the mechs get him?”

“No. Fortunately, I got to him first."

Jacob’s eyes widened, and he shifted into a defensive position, eyes wary and hand surreptitiously near his pistol. "Wait…you killed Wilson? Why?"

Miranda noted the movement, and raised an eyebrow. "Don't worry, Jacob, I'm not going to shoot you. I killed him because he’s the one who sabotaged the security mechs."

"Wait, what? How do you know that?"

"There are very few people here who either have security clearance high enough to access the mechs' programming, or the technical skill to bypass the safeguard systems. Aside from you and me, Wilson is the logical suspect. It wasn't you, and it wasn't me. Ergo, Wilson."

"Hell, Miranda, how do you know it wasn't me?" Jacob seemed to be getting angry now, and his voice had risen. "I could have been the one who did it! I'm the head of security…no one had a better chance to screw up the mechs than me!"

Miranda leveled another glance at him. "Jacob, I didn’t get to where I am without the ability to read people. You wouldn’t have done this. You couldn’t have done this."

Jacob clearly didn’t know whether to take that as a compliment or an insult, but let it go nevertheless. "Still, it doesn’t make sense. Why would he do that?"

Miranda frowned. "I will admit, I would have liked to ask him that. Unfortunately, he pulled a gun on me, and I never got the chance."

"Of course he pulled a gun on you! He knew you would try to kill him!"

"He was right." Miranda held Jacob’s gaze coolly for a few seconds. "He may have been hired to do this by the Shadow Broker. We know he was interested in acquiring Shepard's body for the Collectors. Or it might have been one of Cerberus' own enemies, trying to sabotage a major cell."

She abruptly turned on her heel and went over to the terminal on the desk. With a few taps, a stainless steel slab emerged from the wall, wheeled legs unfolding as it did so. She turned away from the computer and wheeled the gurney over to where what was left of Shepard lay.

"Regardless of who wanted Shepard dead, right now we have to deal with the fact that he is. Again." Miranda looked down at the mess and grimaced. "Let's get him to the docking bay and grab a shuttle. The Illusive Man will want to know about this, if he doesn’t already. Either way, he will not be pleased. Now help me lift the Commander here…"

**Notes for the Chapter:**

> If you’re wondering where Miranda puts those extra thermal clips, given her skintight suit and the apparent lack of pockets, don’t ask me. She clearly must carry spare ammo in the game, as the others do, so she's got to have SOMEWHERE to put it. I like to imagine that during her time on the Lazarus Project she wears a lab coat over her bodysuit, which makes sense for a scientist and also seems much more sensible. (Can you imagine trying to get blood/bodily fluids/whatever other icky byproducts come of raising the dead out of latex/rubber/unstable molecules/whatever the hell Miranda is wearing that rides halfway up her asscrack?)
> 
> As for Shepard’s role in this story…Cerberus still has his body. They’ve already brought him back to life once, from a much worse state than he is currently in at the end of this chapter. (He’s dead again, but at least this time he’s fresh.) Nevertheless, they’re down a Chief Medical Officer who was a major player in that resurrection, not to mention four billion credits, and they don’t have the luxury of another two years before the Reapers invade. So will they be devoting more time and resources to bringing Shepard back again, or not? Only time will tell…


	2. Gone But Not Forgotten

**Summary for the Chapter:**

> Kaidan Alenko and Jeff "Joker" Moreau meet on the second anniversary of Shepard's death. Joker has an interesting message to show Kaidan.

_1500 hours_  
March 15, 2185  
The Dark Star Lounge 

During the day, the "lounge" was fairly quiet. The music was playing at a normal volume rather than the eardrum-pounding levels that it could reach on a busy night, and aside from a couple of asari on the dance floor, there were only a handful of people sitting at tables, drinking quietly.

One of them was Jeff "Joker" Moreau. He sat alone, nursing a beer and occasionally darting glances over to the entrance. When Kaidan Alenko finally walked in, Joker raised his hand in a wave, then returned to his drink. After ordering at the bar, Kaidan came over with his own beer in hand, then pulled out a chair and sat down.

"Long time no see, Joker."

It had been a year since Joker had last seen Kaidan, and the occasion had not been a particularly happy one. On the first anniversary of Shepard's death, the Normandy crew who had been closest to Shepard—well, at least those who hadn't fallen out of contact—had gathered to commemorate his life. Liara had sent a brief message conveying her regret at having "unavoidable responsibilities" on Illium that prevented her from coming—strange, as Liara of all of them had been closest to Shepard. Garrus seemed to have gone completely AWOL; no one had heard from or of him in months. But Kaidan came, and Tali (now Tali'Zorah vas Neema), and even Wrex all the way from Tuchanka. Joker, Dr. Chakwas, and now-Councillor Anderson made for a respectable showing from the non-combat crew.

Anderson volunteered his swanky apartment (being a diplomat apparently had its privileges), and they all sat and drank in an informal memorial, occasionally sharing stories of Shepard. Now in the same room for the first time in a year, the crew found themselves surprisingly awkward with each other at first; in many ways, Shepard had been what brought them together, and it was primarily his memory that now bound them even this loosely.

Somehow, the conversation always drifted back to the same topic: the Reapers, and what to do about them. The Council refused to believe that they existed, even with a member of their own vouching for Shepard's veracity. The Alliance was much the same. But regardless of what the Council or the Alliance thought, the Reapers were coming. Everyone in the room knew this. They'd wasted a year of preparation already, trying to get the message through the bureaucrats' impenetrable walls of denial…what could they do? Continue to bang their heads against those walls in hopes that they would eventually crumble, or somehow find a way to prepare for the Reapers on their own? Everyone left that weekend feeling vaguely dissatisfied, and knowing that if Shepard were still here, he’d be able to think of _something_ , or do _something_ , that would help the galaxy’s chances.

This year was shaping up to be even worse. Liara hadn’t even bothered to send a message this time, while Tali and Wrex both pleaded responsibilities to their respective peoples. Chakwas had been late leaving the med center on Mars due to an emergency and was still en route, while Anderson was spending the day mired in urgent Council affairs. Those two were planning to meet up with them the next day, but today—the official anniversary—Kaidan and Joker were the lone votaries to Shepard’s memory.

"Yeah, it’s been a while. Too bad Chora's Den is gone. It might have been a pit, but that was a bar! This place is all...glossy. Also, the drinks are way more expensive."

"So basically, be honest, you miss the asari dancers." At Joker’s chuckle, Kaidan smirked. "To be fair, we're part of the reason there is no more Chora's Den. Taking out Fist and his operation can't have done much for its continued business, or its clientele."

"Who's 'we'? I'm not the one who went around shooting up bars. Er, not that I'm not glad that you saved Tali, though. Otherwise, who'd fix up the Nor..." Joker trailed off.

There was a moment of silence, and the sparkle of amusement faded from both their eyes. Kaidan leaned forward, elbows resting on the table. "So, Joker, seems like we only see each other on the anniversary anymore."

"Not my fault. I'm not going anywhere." Joker had been in a small Alliance-owned apartment on the Citadel for eight months, on administrative leave. After the Normandy's destruction, the Alliance transferred him to a couple of different ships. It was never the same, though, and both of his COs had been tight-assed idiots who couldn't deal with a pilot who told them what they needed to hear and made no bones about it. Joker sometimes wondered how he'd been lucky enough to stumble into the Normandy gig: what were the odds that he'd get two sane, sensible superiors in a row like Anderson and Shepard, rather than these mouth-breathing idiots? The assignments had...not turned out well, and after the second one ended rather _abruptly_ , Joker found himself grounded. If a Council member hadn't been in his corner, and he hadn't still had the residual goodwill of having worked for the hero of the Citadel, he'd likely have been court-martialed.

"I heard you made Staff Commander, by the way. Congrats." Joker clinked his glass against Kaidan's and gave him a wry smile. "At least one of us is still in the Alliance's good graces."

"I wouldn't go that far," Kaidan replied. "After all, it's in my file that I believe that ancient machines are coming to wipe out the entire galaxy, and I'm pretty sure Anderson's the only reason I haven't been committed as an L2 gone loopy. My CO keeps looking at me like he thinks I'm gonna flip out and start throwing people out the airlock."

Joker grimaced. "Oh, if only I'd been able to throw folks out the airlock on my last assignment. Then it might have been tolerable...and I wouldn't be stuck here on the Citadel."

Kaidan chuckled, then grew sober. "Joker. You said you had important news. Let’s cut the small talk and get to it."

"Wow, you're still so good with people." Joker sighed, then started typing on his omni-tool as he continued. "A week ago I got an extranet message, which somehow bypassed all the usual Alliance spy filters. It didn't say who it was from, but I think I have an idea. They—well, read it."

_To: Flight Lieutenant Jeff Moreau  
From: [SENDER INFORMATION UNAVAILABLE]_

_Mr. Moreau:_

_I am contacting you on behalf of an organization that knows what is coming. Your commander warned the galaxy, and they wouldn’t listen. We did, and are willing to do what is necessary to save it._

_We have an upcoming project that only you can help with, related to your commander and to the galactic threat he warned us of. We would like to talk to you about contributing your unique skills to this project. We are certain we can offer reasonable terms, and can supply whatever financial compensation you require._

_Please think about our offer. We will be in touch._

Kaidan frowned. "An anonymous organization with seemingly bottomless pockets and an interest in Shepard and the Reapers, that is willing to 'do what is necessary'?" It took him about two seconds to come to the same conclusion that Joker had. "Wait. Cerberus contacted you?"

"That's what it sounds like," Joker said. "I guess they must have heard about my amazing skills in the pilot's chair. Either that or they really like the sound of bones breaking."

"You're taking this to Anderson, right?" Kaidan asked. At Joker's silence, he brought his palm to his forehead and half-closed his eyes. "Jesus. At least tell me you're not thinking of signing on with them."

"It's the only way I'm gonna get any action! And at least I'd be able to do something. Do you have any idea how useless I've felt the past four months?"

" _Cerberus_ ," Kaidan growled. "After the experiments we saw them conduct? After the rachni and the thorian creepers? After that thresher maw trap? After Kahoku? I was on the ground for most of those, Joker. Trust me, you don't want to work with Cerberus."

"You got any better ideas? The Reapers are cruising towards Council space and no one's doing anything! Cerberus may be a bunch of crazy, murderous xenophobes, but at least they’re willing to do something. That's more than I can say for the Alliance or the Council."

"Anderson's trying his best with the Council. Given a little more time—"

"Time is one thing we don't have, Kaidan." Joker had meant that to come out sounding angry, but instead he just sounded sad. "We've gotta do something. Now. We don't know when the Reapers are coming, but we know they are. It might be in a hundred years, it might be tomorrow. I’m not really sure where 'dark space' is, or how fast the Reapers can travel. But the Council's not going to believe they exist until one shows up and blasts them in the face. And by then, it'll be too late. As for the Alliance, I imagine they're busy with the vanishing human colonies in the Terminus systems."

Kaidan quirked an eyebrow at Joker. "You know, you shouldn't know about those. I'm pretty sure you don’t have the clearance."

Joker snorted. "Yeah, spend an hour anywhere soldiers congregate and you know. There's been, what, two so far? Supposedly it’s batarian slaver rings...but no real evidence. Just empty colonies. Creepy. But the important thing is, if the Alliance is hung up on all that, they're going to ignore the bigger threat even harder. No, if anyone's gonna do something, it's gotta be us, with or without Cerberus."

"What do you expect us to do? I'm not Shepard. He'd probably have some amazing brainwave or Prothean vision that led to a secret weapon against the Reapers. I'm just a soldier. And I've tried to think of something, anything, but I've come up with nothing. Same with Anderson. And the only idea you've got involves joining an organization that's just as likely to slaughter the majority of the galaxy as to save it."

"At least I've _got_ an idea!" When he noticed the others in the bar looking at them, Joker lowered his voice. "Look, we've got to do something. We can't just sit around with our thumbs up our asses, twiddling away until the killer spaceships come to slaughter us all. If we don't join Cerberus, then we've gotta do something on our own." Anticipating Kaidan's protest, he continued, "And yeah, that means without Council or Alliance approval if necessary."

Kaidan frowned. "You're not gonna back down on this, are you?" At the mutinous expression he received in reply, he sighed. "Fine. Tomorrow we'll ask Anderson if there’s something, anything, we can do. And if not...then I guess we'll see what our options are from there."

"Good. I'll try to figure out what we'll need. Obviously some kind of transport, whatever happens, unless the key to defeating the Reapers is on the Citadel. Which, given the whole Conduit thing, might not be that farfetched. We'll need some sort of fighting team, as I wouldn't be much good in a firefight and I don't think you want to do everything solo. Maintenance and support crew, some kind of supply line for weapons and rations...I'll try to have it ready by the time we talk to Anderson tomorrow."

"Let's not put the cart before the horse here. Let’s talk to Anderson first." Though he continued to frown at Joker, Kaidan found himself a little relieved. At least this would end the wretched, helpless waiting, and they'd be doing _something_.

"Right. Whatever. Anyway, if this works out, I'll tell Cerberus to screw themselves next time they contact me." Joker had no intention of doing any such thing—crazy as Cerberus was, they might need the help—but Kaidan didn't need to know that. He'd keep channels open, and that way, if and when they needed more help than Anderson could give, they'd have it.

Kaidan rose to his feet, leaving his glass half-full. "Then I guess we know what we need to do. And I'll see you tomorrow at Anderson's."

"Tomorrow at Anderson's," Joker echoed. It was _on_.

**Notes for the Chapter:**

> As you can see, the timeline here is already changing; because Shepard’s recovery was going more slowly than in canon, Joker is only now being approached by Cerberus. In the original timeline, Joker was already firmly on board with Cerberus and the new Normandy by the time the second anniversary came around, and hence never had the opportunity for this conversation with Kaidan.
> 
> And yes, Anderson’s apartment is the one from the Citadel DLC.


End file.
